Habit makes copper most upset (6)
I believe the answer is:
Here is my best explanation:
'habit' is the definition.
(I've seen this before)
'copper most upset' is the subsidiary indication.
'copper' becomes 'cu' ('Cu' can be a synonym of 'copper').
'upset' is an anagram indicator.
'most' with letters rearranged gives 'stom'.
'makes' is the link.
(Other definitions for custom that I've seen before include "Regular trade", "Habit, usage", "Tradition; habit", "Habitual action", "Use", "Regular process", "'Habit, practice (6)'", "Habitual patronage", "Traditional usage" and "Usual way of doing something".)